In the paper, different morphologies of bainite were obtained through isothermal quenching at 320°C and 395°C in a medium-carbon carbide-free bainitic steel. The cyclic deformation mechanism was explored by using low cycle fatigue testing. The volume fraction of retained austenite was measured by X-ray diffraction and the space partitioning of the solute atoms was constructed by three-dimensional atom probe. Results showed that the fatigue life at 320°C was always higher than that at 395°C under low and high total strain amplitude. The cyclic softening at the early fatigue stage increased the plastic strain of the sample which was responsible for the reduction of the fatigue life at 395°C. Strain-induced retained austenite to martensite contributed to initial cyclic hardening, but almost having no effect on the subsequent cyclic stable/softening behaviors. The finer bainitic ferrite sheaves obtained at 320°C changed the small fatigue crack propagation direction and delayed the crack propagation rate, which was beneficial for the fatigue properties. In addition, the substitutional atoms did not redistribute between the retained austenite and bainitic ferrite before and after cyclic deformation.